scverse / scverse/scanpy

Tha maximal number of iterations maxit (set to 20 by the program) allowed for finding a smoothing spline with fp=s has been reached

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Description

I was trying to plot a heatmap using this command:
ax=sc2.pl.heatmap(adata, sorted_unique_marker_genes, groupby='ident', use_raw=False, vmin=-3, vmax=3, cmap='bwr',show=True, var_group_rotation=0, dendrogram=True, save='ClusterMap.png')

And it didn't finish running after an overnight, with the following warning message:
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set show_gene_labels=True
/usr/local/lib/python3.6/dist-packages/scipy/interpolate/fitpack2.py:227: UserWarning:
The maximal number of iterations maxit (set to 20 by the program)
allowed for finding a smoothing spline with fp=s has been reached: s
too small.
There is an approximation returned but the corresponding weighted sum
of squared residuals does not satisfy the condition abs(fp-s)/s < tol.
warnings.warn(message)

I don't understand why this is taking this long because seaborn was able to finish plotting within 30 minutes. Do you know why?

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Research direction

Start by reproducing the provided sc2.pl.heatmap command with dendrogram=True and save='ClusterMap.png', then inspect the reported scipy.interpolate/fitpack2 warning and compare the runtime with seaborn. Done would require identifying why the heatmap does not finish and defining a specific, reproducible change or documentation update.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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